[BioC] problems running DEXseq

Wolfgang Huber whuber at embl.de
Sun Jun 30 10:27:05 CEST 2013

Dear Diya

it appears that you are running dexseq_count.py as if it were a shell script, rather than from Python. As a consequence, the first line of the script is interpreted as the Linux command 'import' rather than as Python code, leading to the error you report.

It also seems a bit troubling that you run this code as a superuser. That should never be necessary.

Maybe best would be for you to hook up locally with a sys admin or with someone knowledgeable in Unix scripting, since it seems difficult to diagnose your particular system architecture remotely.

	Best wishes

On Jun 29, 2013, at 1:32 am, Diya <dvaka at stanford.edu> wrote:

> Hi,
> We want to explore DEXseq to see if we find anything interesting for alt-
> splicing analysis. I have aligned the reads using iGenomes UCSC genome files 
> for hg19 genome. We have 2 Control and 3 KD samples( biological replicates).
> I have successfully passed the first step where in I prepapred the annotation 
> file.
> The second step which is "for counting " I encounter errors. 
> The command used is 
> sudo samtools view ./Control_N1/Control_N1_thout/accepted_hits.sorted.bam | 
> /data1/Bethsaida/python_scripts/dexseq_count.py -p yes 
> HS.GRCh37.72_norm.DEXSeq.gff - combined.txt
> Error message:
> import: unable to open X server `' @ error/import.c/ImportImageCommand/366.
> /data1/Bethsaida/python_scripts/dexseq_count.py: line 3: syntax error near 
> unexpected token `('
> /data1/Bethsaida/python_scripts/dexseq_count.py: line 3: `optParser = 
> optparse.OptionParser( '
> Any help, so that I can start running the next steps.
> Thanks,
> Diya
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